Clipping border doesn't work properly
You got "Snap during transform" enabled (magnet icon) and when you're moving vertices with "G" it snaps them to the nearest surface (cause you have also Face as the type of element to snap to enabled) As this are edge vertices, and you're doing it from considerable distance, it snaps not to the edge faces but to back faces. I would suggest you to try disable first one and snap vertices with CTRL. It would also be helpful to decrease distance to increase accuracy or hide back faces of high poly model to avoid snapping to the wrong ones. You could do it with mask modifier for example.Options, which I'm talking about are selected in the image.